Otto Addo named a very predictable team for the game, with captain Adre Ayew returning to the starting line-up.
Abdul Baba Rahman also started at left-back and formed part of the back-four that also featured Denis Odoi, Gideon Mensah and Daniel Amartey.
In the absence of the injured Thomas Partey, Baba Iddrisu started in defensive midfield while Andre Ayew and Kudus played as double central midfielders.
Afena-Gyan started his third game in a row as Ghana’s leading striker and was flanked by Jordan Ayew to the left and Abdul Fatawu Issahaku to the right.
The Black Stars made a strong start to the game and dominated the early exchanges as Madagascar preferred to sit back.
The first opening of the game fell to Issahaku, who beautifully cut inside only to fire a left-footed shot into the side net.
Afena-Gyan was the next to go close after being played through on goal but the Roma striker hesitated, allowing his marker to block his shot with a timely tackle.
Despite dominating possession, Ghana’s first shot on target came after the hour mark when Jordan Ayew shrugged off his marker and shot from 35 yards but his effort was punched away by the Malagasy goalkeeper.
A minute later, Iddrisu also went close when his goal-bound header was saved. Madagascar’s first real incursion into Ghana’s box came late in the first half, but they were unable to convert.
The Black Stars’ quest for a goal ended nine minutes after the restart, with Kudus coolly tapping home following a cutback by Afena-Gyan.
The AS Roma teenager went from provider to scorer a minute later when he prodded the ball into the net after applying a first-time finish to Mensah’s cross, while substitute Bukari added a third late on.
Madagascar rarely threatened Ghana’s defence in the final half-hour as the Black Stars ran out as 3-0 winners to move to the top of Group C in the 2023 AFCON qualifiers.
Meanwhile, Bristol City forward Antoine Semenyo came on in the second half to mark his international debut. The Black Stars will face the Central African Republic (CAR) in their next qualifying game on Sunday.
